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[[Category:Software]]
[[Category:Software]]
= Summary Files Specification for RAREMETAL =
RAREMETAL use summary statistics files to perform meta-analysis. These includes (1) score statistics file and (2) covariance file.
RAREMETAL use summary statistics files to perform meta-analysis. These includes (1) score statistics file and (2) covariance file.
Both [[RAREMETALWORKER|RAREMETALWORKER]] and [http://genome.sph.umich.edu/wiki/Rvtests '''rvtests'''] can generate these summary statistics files.
Both [[RAREMETALWORKER|RAREMETALWORKER]] and [http://genome.sph.umich.edu/wiki/Rvtests '''rvtests'''] can generate these summary statistics files.
== Input score test statistics file ==
== Input score test statistics file ==
=== Format ===
Header lines begins with '#' or 'CHROM'. After header part, we listed the meaning of each column as following:
Header lines begins with '#' or 'CHROM'. After header part, we listed the meaning of each column as following:
# PVALUE P-value
# PVALUE P-value
=== RAREMETALWORKER ===
RAREMETALWORKER generates prefix.traitName.singlevar.score.txt, e.g. prefix.HDL.singlevar.score.txt
##ProgramName=RareMetalWorker
##ProgramName=RareMetalWorker
1 565111 T C 2778 0.0170986 0.0170986 95 1 4.19613e-102 2730 1 47 24.0897 13.6258 0.129688 0.0770708
1 565111 T C 2778 0.0170986 0.0170986 95 1 4.19613e-102 2730 1 47 24.0897 13.6258 0.129688 0.0770708
=== Rvtests ===
Rvtests generates prefix.MetaScore.assoc, e.g. prefix.MetaScore.assoc
##Samples=2659
##Samples=2659
Covariance test statistics contains the LD matrix among a variant and the adjacent markers within a prefixed-sized window. The default window size is 1MB. It has the following format:
Covariance test statistics contains the LD matrix among a variant and the adjacent markers within a prefixed-sized window. The default window size is 1MB. It has the following format:
=== Format ===
# CHROM Chromosome
# CHROM Chromosome
# COV (rvtests only) Covariance matrix between test statistics
# COV (rvtests only) Covariance matrix between test statistics
=== RAREMETALWORKER ===
RAREMETALWORKER generates prefix.traitName.singlevar.cov.txt, e.g. prefix.HDL.singlevar.cov.txt
CHR POS VAR_POS_IN_WINDOW LD_MATRIX
CHR POS VAR_POS_IN_WINDOW LD_MATRIX
1 878744 878744,879381,1560000,1864659,1877659 0.000404537,-0.000235215,-1.4455e-05,-8.69137e-06,-3.1027e-05,
1 878744 878744,879381,1560000,1864659,1877659 0.000404537,-0.000235215,-1.4455e-05,-8.69137e-06,-3.1027e-05,
=== Rvtests ===
Rvtests generates prefix.MetaCov.assoc.gz, e.g. prefix.HDL.MetaCov.assoc.gz
Later version of rvtests will also generate tabix index file, prefix.MetaCov.assoc.gz
Later version of rvtests will also generate tabix index file, prefix.MetaCov.assoc.gz
1 878744 1877659 5 878744,879381,1560000,1864659,1877659 0.000404537,-0.000235215,-1.4455e-05,-8.69137e-06,-3.1027e-05
1 878744 1877659 5 878744,879381,1560000,1864659,1877659 0.000404537,-0.000235215,-1.4455e-05,-8.69137e-06,-3.1027e-05
= Contact =
Please contact Dajiang Liu ([mailto:dajiang@umich.edu]), Xiaowei Zhan ([mailto:zhanxw@umich.edu]), Shuang Feng([mailto:sfengsph@umich.edu]) or Goncalo Abecasis ([mailto:goncalo@umich.edu]).
Please contact Dajiang Liu ([mailto:dajiang@umich.edu]), Xiaowei Zhan ([mailto:zhanxw@umich.edu]), Shuang Feng([mailto:sfengsph@umich.edu]) or Goncalo Abecasis ([mailto:goncalo@umich.edu]).
